Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human.

At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value.

F8 gene inversion and duplication cause no obvious hemophilia A phenotype.

Hemophilia A (HA, OMIM#306700) is an X-linked recessive bleeding disorder caused by the defects in the F8 gene, which encodes coagulation factor VIII (FVIII). Intron 22 inversion (Inv22) is found in about 45% of patients with severe hemophilia A. Here, we reported a male without obvious hemophilia A phenotype but bearing an inherited segmental variant duplication encompassing F8 as well as Inv22. The duplication was approximately 0.16 Mb and involved from exon 1 to intron 22 of F8. This partial duplication and Inv22 in F8 was first found in the abortion tissue of his older sister with recurrent miscarriage. The genetic testing of his family revealed that his phenotypically normal older sister and mother also had this heterozygous Inv22 and a 0.16 Mb partial duplication of F8, while his father was genotypically normal. The integrity of the F8 gene transcript was verified by sequencing of the adjacent exons at the inversion breakpoint, which explained why this male had no phenotype for hemophilia A. Interestingly, although he had no significant hemophilia A phenotype, the expression of C1QA in his mother, sister, and the male subject was only about half of that in his father and normal population. Our report broadens the mutation spectrum of F8 inversion and duplication and its pathogenicity in hemophilia A.

Patient-derived avian influenza A (H5N6) virus is highly pathogenic in mice but can be effectively treated by anti-influenza polyclonal antibodies.

Highly pathogenic avian influenza A (H5N6) virus has been circulating in poultry since 2013 and causes sporadic infections and fatalities in humans. Due to the re-occurrence and continuous evolution of this virus subtype, there is an urgent need to better understand the pathogenicity of the H5N6 virus and to identify effective preventative and therapeutic strategies. We established a mouse model to evaluate the virulence of H5N6 A/Guangzhou/39715/2014 (H5N6/GZ14), which was isolated from an infected patient. BALB/c mice were inoculated intranasally with H5N6/GZ14 and monitored for morbidity, mortality, cytokine production, lung injury, viral replication, and viral dissemination to other organs. H5N6/GZ14 is highly pathogenic and can kill 50% of mice at a very low infectious dose of 5 plaque-forming units (pfu). Infection with H5N6/GZ14 showed rapid disease progression, viral replication to high titers in the lung, a strongly induced pro-inflammatory cytokine response, and severe lung injury. Moreover, infectious H5N6/GZ14 could be detected in the heart and brain of the infected mice. We also demonstrated that anti-influenza polyclonal antibodies generated by immunizing rhesus macaques could protect mice from lethal infection. Our results provide insights into the pathogenicity of the H5N6 human isolate.

Association between IRGM polymorphisms and tuberculosis risk: A meta-analysis.

BACKGROUND: The human immunity-related GTPase M (IRGM) is involved in regulating autophagy against invading pathogens. Recently, inconsistent results have been reported about the association between IRGM polymorphisms and tuberculosis risk in several studies. METHODS: We searched the PubMed, Embase, and Web of Knowledge, and extracted data from eligible articles to estimate the associations between IRGM polymorphisms (rs10065172, rs4958842, rs4859843, rs4859846, and rs72553867) and tuberculosis risk. The pooled odds ratio (OR) with 95% confidence intervals (CIs) were calculated using Review manager 5.3. The studies heterogeneity was assessed by Cochran Q test. Funnel plot, Begg test, and Egger linear regression test were used to evaluate the publication bias. RESULTS: Nine case-control studies in 8 articles involving 3780 tuberculosis and 4835 control were analyzed. The analysis showed that IRGM rs10065172 and rs4859846 were significantly associated with tuberculosis risk in all genetic models whereas the latent tuberculosis infection group in 1 study was excluded. However, stratified analysis revealed significant associations for IRGM rs10065172 in all genetic models among Asians, but not for African/African-Americans. Significant associations were observed in recessive and dominant model for rs4958842, allele and recessive model for rs4859843, and all genetic models for rs4859846. No significant associations between rs72553867 polymorphism and tuberculosis risk was identified. Publication bias was detected in allele and additive model of rs4859843. CONCLUSIONS: IRGM rs10065172 was associated with decreased risk of tuberculosis in Asian populations, but not in African/Africa-Americans. rs4958842, rs4859843, and rs4859846, had a large protective effect in Asians, whereas rs72553867 was not associated with tuberculosis risk.